Bioinformatics Analyst III

Fred Hutchinson Cancer Center is an independent, nonprofit organization providing adult cancer treatment and groundbreaking research focused on cancer and infectious diseases. Based in Seattle, Fred Hutch is the only National Cancer Institute-designated cancer center in Washington.

With a track record of global leadership in bone marrow transplantation, HIV/AIDS prevention, immunotherapy and COVID-19 vaccines, Fred Hutch has earned a reputation as one of the world's leading cancer, infectious disease and biomedical research centers. Fred Hutch operates eight clinical care sites that provide medical oncology, infusion, radiation, proton therapy and related services, and network affiliations with hospitals in five states. Together, our fully integrated research and clinical care teams seek to discover new cures to the world's deadliest diseases and make life beyond cancer a reality.

At Fred Hutch we value collaboration, compassion, determination, excellence, innovation, integrity and respect. Our mission is directly tied to the humanity, dignity and inherent value of each employee, patient, community member and supporter. Our commitment to learning across our differences and similarities make us stronger. We seek employees who bring different and innovative ways of seeing the world and solving problems.

The Bioinformatics Analyst III will provide data analysis services to researchers in the Fred Hutch Clinical Testing Labs - Molecular OncologyXXXX lab, particularly focusing on molecular, single cell genomics, integration of high-dimensional immunologic data and genome sequencing. This position requires the ability to work independently, manage multiple overlapping demands, and communicate effectively with faculty, lab managers, lab staff, staff scientist, and research staff on a wide range of topics in biology, analytical biochemistry, sound experimental design, and data science. The Bioinformatics Analyst will work closely with the medical director, clinical laboratory director, and MO staff for clinical variant analysis as well as development and execution of small programming and database projects related to the data analysis workflows needed for the Fred Hutch clinical testing labs. The BA is also expected to work closely with NIH teams, Fred Hutch IT teams, Shared Resources cores, especially Genomics and Hutch Data core, and as needed SWOG data teams, to ensure that data quality is high and that users have access to advice and continuing dialog as they review results. Given the large volumes and diverse types of data generated and integrated in Bioinformatics projects, practical applied programming skills are also essential.

PRIMARY/ESSENTIAL DUTIES:

Supports the maintenance of computational infrastructure and the flow of samples and information for large-scale studies in compliance with applicable FDA, NYS-DOH, CLIA, and CAP regulations.
• Contribute to web-based bioinformatics (both public and internal relational databases), and assists in the development as well as the application of computational tools.
• Interpret complex biological information, conduct statistical and genomic analysis.
• Write custom scripts to access databases, perform and evaluate quality control and analyze sequencing data (must be proficient with NGS, LRS data would be a desirable skill).
• Assist in the development and refinement of data analysis and integration methodology and pipelines. Must have ability to write scripts automating data transfers to and from AWS and other databases, and can incorporate API.
• Analyze large sequence datasets from diverse workflows including exome capture, RNA-seq, single cell sequencing, ATAC-seq, and CRISPR screens.
• Work with Hutch scientists to refine computational research questions and develop analytical processes that can be applied to these genomic datasets.
• Consult with researchers on sound experimental design.
• Identify appropriate bioinformatics tools to meet the needs of proposed projects.
• Partner with researchers who are developing novel assays to design appropriate processing and analysis workflows.
• Review current literature to identify and adopt software and methodologies, making new analysis capabilities available to the team.
• Provide figures and written sections to document methods and results for manuscripts, presentations, and grant applications.
• Collaborate with colleagues in the Genomics Shared Resource and the Hutch Data Core to ensure the integrity and consistency of primary data, track experimental methods and metadata, define standardized analysis pipelines, and provide support as stakeholders analyze and interpret results.
• Train laboratory members and collaborators on analytic workflows.
• Upload and maintain datasets, workflows, and code (for example GEO, Github).
• Excellent written and oral communication skills - required for manuscripts, grant, presentation, preparation.
• Candidate must demonstrate outstanding personal initiative and creativity in problem solving.
• Other duties as assigned.

SCOPE OF RESPONSIBILITY:

• Level of autonomy: A senior level position that works under minimal supervision, works on and completes complex projects requiring advanced knowledge and skills. Ability to conduct clinical variant analysis as part of the clinical data review team, manage multiple overlapping demands, work independently as well as balance their own schedules, and communicate effectively with faculty, managers, lab staff, and research staff on a wide range of topics in molecular biology, analytical biochemistry, sound experimental design, and data science.
• Financial responsibility: None

MINIMUM QUALIFICATIONS:

• Bachelor's degree in bioinformatics, computational biology, genetics, or related field.
• At least three years' direct experience in computational analysis of large, complex sequence-based molecular data sets.
• Two+ years of experience in software development, data engineering, data science, or related field with a track record of manipulating, processing, and extracting value from large datasets.
• Direct experience must include whole exome sequencing, analysis of bulk RNA-seq data with multiple contrasts, analysis of multimodal single-cell immune repertoire profiling data, gene set enrichment, and integration of data across multiple modalities (e.g., epigenetic profiling, TCR-seq, CITE-seq, ChIP-seq, ATAC-seq, and CRISPR/Cas9 knockout screens).
• Demonstrated fluency in R and Python 3 are essential.
• Proficiency with Linux/Unix shell scripting (e.g., bash).
• Facility with commonly used Bioconductor packages, ggplot, tidyverse etc.
• Ability to generate and customize common data visualizations (PCA plots, volcano plots, Circos plots, etc).
• Familiarity with workflow and scheduling software (e.g., Slurm).
• Excellent written and verbal communication skills.

PREFERRED QUALIFICATIONS:

• Master's degree in bioinformatics, computational biology, genetics, or related field.
• Experience handling data in compliance with FDA, NYS-DOH, CAP, and CLIA regulations.

The annual base salary range for this position is from $95,888 to $143,811, and pay offered will be based on experience and qualifications.

Fred Hutchinson Cancer Center offers employees a comprehensive benefits package designed to enhance health, well-being, and financial security. Benefits include medical/vision, dental, flexible spending accounts, life, disability, retirement, family life support, employee assistance program, onsite health clinic, tuition reimbursement, paid vacation (12-22 days per year), paid sick leave (12-25 days per year), paid holidays (13 days per year), paid parental leave (up to 4 weeks), and partially paid sabbatical leave (up to 6 months).